well, there are two wires between the cdi and the reg/rec and 2 wires from the alternator directly to the cdi. the bike won't run with the reg/rec disconnected, but i don't think that necessarily means it can't be wired differently with separate modules or otherwise.
http://www.trialspartsusa.com/diagrams/DUCATIdigital2004.jpg
I think I'll try the $0.35 diode first...it's pretty obvious on mine which one burned out and will replace both while I'm at it. i think radioshack sells a circuit sealing lacquer spray. Maybe I'll seal it first with that then fill with silicone rtv (I don't know how silicone would affect any electronics). The actual potting/encapsulating epoxy is expensive stuff!